Microbiome and multi-omics snakemake workflows

General overview

The workflows displayed in this document define the snakemake rules in a DAG (directed acyclic graph) format. You may find a link to the interactive snakemake HTML report in some workflow. The link will enable you to explore the workflow and associated statistics. While exploring the interactive workflow, you can close the left bar (the overlap) to get a more expansive display view.

IMAP-PART 01

Software requirement for microbiome data analysis


Explore the IMAP-PART 01 interactive snakemake report (if available) here.


IMAP-PART 02

Exploring and profiling SRA sample metadata


Explore the IMAP-PART 02 interactive snakemake report (if available) here.


IMAP-PART 03

Downloading SRA FastQ reads using fasterq-dump


Explore the IMAP-PART 03 interactive snakemake report (if available) here.


IMAP-PART 04

Quality Control of Sequencing Reads


Explore the IMAP-PART 04 interactive snakemake report (if available) here.


IMAP-PART 05

Microbial profiling with MOTHUR pipeline


Explore the IMAP-PART 05 interactive snakemake report (if available) here.


IMAP-PART 06

Microbial profiling with QIIME2 pipeline


Explore the IMAP-PART 06 interactive snakemake report (if available) here.


IMAP-PART 07

Data processing for download analysis


Explore the IMAP-PART 07 interactive snakemake report (if available) here.

IMAP-PART 08

Data exploration and visualization


Explore the IMAP-PART 08 interactive snakemake report (if available) here.



Multi-Omics data analysis

…BRIEF INTRO IN PROGRESS…


Citation

Please consider citing the iMAP article[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.


References

[1]
Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4


Appendix

Project main tree

.
├── LICENSE
├── README.md
├── config
│   ├── config.yml
│   ├── pbs
│   │   ├── cluster.yaml
│   │   └── config.yaml
│   ├── samples.tsv
│   ├── slurm
│   │   ├── cluster.yaml
│   │   └── config.yaml
│   └── units.tsv
├── dags
│   ├── rulegraph.png
│   └── rulegraph.svg
├── images
│   ├── bioinformatics.png
│   ├── bkgd.png
│   ├── imap.png
│   ├── imap_part01.svg
│   ├── imap_part02.svg
│   ├── imap_part03.svg
│   ├── imap_part04.svg
│   ├── imap_part05.svg
│   ├── imap_part06.svg
│   ├── imap_part07.svg
│   ├── imap_part08.svg
│   ├── rulegraph.png
│   └── smkreport
│       └── screenshot.png
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── export.bib
│   ├── imap.bib
│   └── references.bib
├── report.html
├── results
│   └── project_tree.txt
├── smk.css
├── styles.css
└── workflow
    ├── Snakefile
    ├── envs
    │   ├── environment.yml
    │   ├── mothur.yml
    │   └── qiime220232.yml
    ├── report
    │   ├── biobakery.rst
    │   ├── explore.rst
    │   ├── imap.rst
    │   ├── mothur.rst
    │   ├── process.rst
    │   ├── qiime2.rst
    │   ├── readqc.rst
    │   ├── rsmkrpt.rst
    │   ├── software.rst
    │   ├── sracache.rst
    │   ├── srametadata.rst
    │   ├── srareads.rst
    │   └── workflow.rst
    ├── rules
    │   ├── render_index.smk
    │   ├── report.smk
    │   ├── rmd_report.smk
    │   └── rules_dag.smk
    └── scripts
        ├── README.md
        ├── files4smk_report.sh
        ├── render.R
        ├── rules_dag.sh
        ├── smk_html_report.sh
        └── tree.sh

14 directories, 60 files



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